Ecological and evolutive implications of bacterial defences against predators

Sustainable strategies: Nature-based solutions to tackle antibiotic resistance gene proliferation and improve agricultural productivity and soil quality

The issue of antibiotic resistance is now recognized by the World Health Organisation (WHO) as one of the major problems in human health. Although its effects are evident in the healthcare settings, the root cause should be traced back to the One Health link, extending from animals to the environment. In fact, the use of organic fertilizers in agroecosystems represents one, if not the primary, cause of the introduction of antibiotics and antibiotic-resistant bacteria into the soil. Since the concentrations of antibiotics introduced into the soil are residual, the agroecosystem has become a perfect environment for the selection and proliferation of antibiotic resistance genes (ARGs). The continuous influx of these emerging contaminants (i.e., antibiotics) into the agroecosystem results in the selection and accumulation of ARGs in soil bacteria, occasionally giving rise to multi-resistant bacteria. These bacteria may harbour ARGs related to various antibiotics on their plasmids. In this context, these bacteria can potentially enter the human sphere when individuals consume food from contaminated agroecosystems, leading to the acquisition of multi-resistant bacteria. Once introduced into the nosocomial environment, these bacteria pose a significant threat to human health. In this review, we analyse how the use of digestate as an organic fertilizer can mitigate the spread of ARGs in agroecosystems. Furthermore, we highlight how, according to European guidelines, digestate can be considered a Nature-Based Solution (NBS). This NBS not only has the ability to mitigate the spread of ARGs in agroecosystems but also offers the opportunity to further improve Microbial-Based Solutions (MBS), with the aim of enhancing soil quality and productivity.

Exploring the microbial savanna: predator-prey interactions in the soil

Soil ecosystems consist of complex multi-trophic communities of predator and prey microbial species. This Comment proposes that integrative approaches are powerful for understanding predator-prey interactions and for revealing how these interactions shape population dynamics in soil communities.

Lifecycle of a predatory bacterium vampirizing its prey through the cell envelope and S-layer

Predatory bacteria feed upon other bacteria in various environments. Bdellovibrio exovorus is an obligate epibiotic predator that attaches on the prey cell surface, where it grows and proliferates. Although the mechanisms allowing feeding through the prey cell envelope are unknown, it has been proposed that the prey's proteinaceous S-layer may act as a defensive structure against predation. Here, we use time-lapse and cryo-electron microscopy to image the lifecycle of B. exovorus feeding on Caulobacter crescentus. We show that B. exovorus proliferates by non-binary division, primarily generating three daughter cells. Moreover, the predator feeds on C. crescentus regardless of the presence of an S-layer, challenging its assumed protective role against predators. Finally, we show that apparently secure junctions are established between prey and predator outer membranes.

Costs of being a diet generalist for the protist predator Dictyostelium discoideum

Consumers range from specialists that feed on few resources to generalists that feed on many. Generalism has the clear advantage of having more resources to exploit, but the costs that limit generalism are less clear. We explore two understudied costs of generalism in a generalist amoeba predator, Dictyostelium discoideum, feeding on naturally co-occurring bacterial prey. Both involve costs of combining prey that are suitable on their own. First, amoebas exhibit a reduction in growth rate when they switched to one species of prey bacteria from another compared to controls that experience only the second prey. The effect was consistent across all six tested species of bacteria. These switching costs typically disappear within a day, indicating adjustment to new prey bacteria. This suggests that these costs are physiological. Second, amoebas usually grow more slowly on mixtures of prey bacteria compared to the expectation based on their growth on single prey. There were clear mixing costs in three of the six tested prey mixtures, and none showed significant mixing benefits. These results support the idea that, although amoebas can consume a variety of prey, they must use partially different methods and thus must pay costs to handle multiple prey, either sequentially or simultaneously.

Predatory protists reduce bacteria wilt disease incidence in tomato plants

Soil organisms are affected by the presence of predatory protists. However, it remains poorly understood how predatory protists can affect plant disease incidence and how fertilization regimes can affect these interactions. Here, we characterise the rhizosphere bacteria, fungi and protists over eleven growing seasons of tomato planting under three fertilization regimes, i.e conventional, organic and bioorganic, and with different bacterial wilt disease incidence levels. We find that predatory protists are negatively associated with disease incidence, especially two ciliophoran Colpoda OTUs, and that bioorganic fertilization enhances the abundance of predatory protists. In glasshouse experiments we find that the predatory protist Colpoda influences disease incidence by directly consuming pathogens and indirectly increasing the presence of pathogen-suppressive microorganisms in the soil. Together, we demonstrate that predatory protists reduce bacterial wilt disease incidence in tomato plants via direct and indirect reductions of pathogens. Our study provides insights on the role that predatory protists play in plant disease, which could be used to design more sustainable agricultural practices.

Predation in a Microbial World: Mechanisms and Trade-Offs of Flagellate Foraging

Heterotrophic nanoflagellates are the main consumers of bacteria and picophytoplankton in the ocean and thus play a key role in ocean biogeochemistry. They are found in all major branches of the eukaryotic tree of life but are united by all being equipped with one or a few flagella that they use to generate a feeding current. These microbial predators are faced with the challenges that viscosity at this small scale impedes predator-prey contact and that their foraging activity disturbs the ambient water and thus attracts their own flow-sensing predators. Here, I describe some of the diverse adaptations of the flagellum to produce sufficient force to overcome viscosity and of the flagellar arrangement to minimize fluid disturbances, and thus of the various solutions to optimize the foraging-predation risk trade-off. I demonstrate how insights into this trade-off can be used to develop robust trait-based models of microbial food webs.

Role of Microbial Volatile Organic Compounds in Promoting Plant Growth and Disease Resistance in Horticultural Production

Microbial volatile organic compounds (MVOCs) are a diverse group of volatile organic compounds that microorganisms may produce and release into the environment. These compounds have both positive and negative effects on plants, as they have been shown to be effective at mitigating stresses and functioning as immune stimulants. Furthermore, MVOCs modulate plant growth and systemic plant resistance, while also serving as attractants or repellents for insects and other stressors that pose threats to plants. Considering the economic value of strawberries as one of the most popular and consumed fruits worldwide, harnessing the benefits of MVOCs becomes particularly significant. MVOCs offer cost-effective and efficient solutions for disease control and pest management in horticultural production, as they can be utilized at low concentrations. This paper provides a comprehensive review of the current knowledge on microorganisms that contribute to the production of beneficial volatile organic compounds for enhancing disease resistance in fruit products, with a specific emphasis on broad horticultural production. The review also identifies research gaps and highlights the functions of MVOCs in horticulture, along with the different types of MVOCs that impact plant disease resistance in strawberry production. By offering a novel perspective on the application and utilization of volatile organic compounds in sustainable horticulture, this review presents an innovative approach to maximizing the efficiency of horticultural production through the use of natural products.

Protistan predation selects for antibiotic resistance in soil bacterial communities

Understanding how antibiotic resistance emerges and evolves in natural habitats is critical for predicting and mitigating antibiotic resistance in the context of global change. Bacteria have evolved antibiotic production as a strategy to fight competitors, predators and other stressors, but how predation pressure of their most important consumers (i.e., protists) affects soil antibiotic resistance genes (ARGs) profiles is still poorly understood. To address this gap, we investigated responses of soil resistome to varying levels of protistan predation by inoculating low, medium and high concentrations of indigenous soil protist suspensions in soil microcosms. We found that an increase in protistan predation pressure was strongly associated with higher abundance and diversity of soil ARGs. High protist concentrations significantly enhanced the abundances of ARGs encoding multidrug (oprJ and ttgB genes) and tetracycline (tetV) efflux pump by 608%, 724% and 3052%, respectively. Additionally, we observed an increase in the abundance of numerous bacterial genera under high protistan pressure. Our findings provide empirical evidence that protistan predation significantly promotes antibiotic resistance in soil bacterial communities and advances our understanding of the biological driving forces behind the evolution and development of environmental antibiotic resistance.

Nonribosomal peptides protect Pseudomonas nunensis 4A2e from amoebal and nematodal predation

The rhizosphere is a highly competitive environment forcing bacteria to evolve strategies to oppose their enemies. The production of toxic secondary metabolites allows bacteria to counteract predators. In this study, we describe the anti-predator armamentarium of the soil-derived bacterium Pseudomonas nunensis 4A2e. Based on a genome mining approach, we identified several biosynthetic gene clusters coding for nonribosomal peptide synthetases. Generation of gene deletion mutants of the respective clusters shows a loss of defense capabilities. We isolated the novel lipopeptides keanumycin D and nunapeptins B and C, and fully elucidated their structures by a combination of in-depth mass spectrometry experiments, stable isotope labelling, and chemical synthesis. Additionally, investigation of the quorum sensing-dependent biosynthesis allowed us to elucidate parts of the underlying regulation of the biosynthetic machinery. Ecology-inspired bioassays highlight the role of these peptides as a defence strategy against protozoans and led us to find a previously unknown function against the bacterivorous nematode Oscheius myriophilus.

Linking Groundwater to Surface Discharge Ecosystems: Archaeal, Bacterial, and Eukaryotic Community Diversity and Structure in Quebec (Canada)

Aquifer systems are composed of water flowing from surface recharge areas, to the subsurface and back to the surface in discharge regions. Groundwater habitats harbor a large microbial biomass and diversity, potentially contributing to surface aquatic ecosystems. Although this contribution has been widely studied in marine environments, very little is known about the connection between underground and surface microbial communities in freshwater settings. Therefore, in this study, we used amplicon sequencing to analyze the archaeal, bacterial, and eukaryotic community diversity and structure in groundwater and surface water samples, spanning the vast regions of the Laurentides and Lanaudières in the Quebec province (Canada). Our results show significant differences between subsurface and surface taxa; with more fungi, Amoebozoa, and chemolithoautotrophic prokaryotes involved in nitrogen-, sulfur-, and iron-cycling dominating the underground samples; while algae, ciliates, methanogens, and Actinobacteria dominate the surface discharge waters. Microbial source tracking suggested that only a small portion of the microbial communities in the groundwater contributed to the surface discharge communities. However, many taxa were shared between both habitats, with a large range of functional diversity, likely explaining their survival in both subsurface and surface water ecosystems.

Root Niches of Blueberry Imprint Increasing Bacterial-Fungal Interkingdom Interactions along the Soil-Rhizosphere-Root Continuum

Plant root-associated microbiomes play critical roles in promoting plant health, productivity, and tolerance to biotic/abiotic stresses. Blueberry (Vaccinium spp.) is adapted to acidic soils, while the interactions of the root-associated microbiomes in this specific habitat under various root microenvironments remain elusive. Here, we investigated the diversity and community composition of bacterial and fungal communities in various blueberry root niches (bulk soil, rhizosphere soil, and root endosphere). The results showed that blueberry root niches significantly affected root-associated microbiome diversity and community composition compared to those of the three host cultivars. Deterministic processes gradually increased along the soil-rhizosphere-root continuum in both bacterial and fungal communities. The co-occurrence network topological features showed that both bacterial and fungal community complexity and intensive interactions decreased along the soil-rhizosphere-root continuum. Different compartment niches clearly influenced bacterial-fungal interkingdom interactions, which were significantly higher in the rhizosphere, and positive interactions gradually dominated the co-occurrence networks from the bulk soil to the endosphere. The functional predictions showed that rhizosphere bacterial and fungal communities may have higher cellulolysis and saprotrophy capacities, respectively. Collectively, the root niches not only affected microbial diversity and community composition but also enhanced the positive interkingdom interactions between bacterial and fungal communities along the soil-rhizosphere-root continuum. This provides an essential basis for manipulating synthetic microbial communities for sustainable agriculture. IMPORTANCE The blueberry root-associated microbiome plays an essential role in its adaptation to acidic soils and in limiting the uptake of soil nutrients by its poor root system. Studies on the interactions of the root-associated microbiome in the various root niches may deepen our understanding of the beneficial effects in this particular habitat. Our study extended the research on the diversity and composition of microbial communities in different blueberry root compartment niches. Root niches dominated the root-associated microbiome compared to that of the host cultivar, and deterministic processes increased from the bulk soil to the endosphere. In addition, bacterial-fungal interkingdom interactions were significantly higher in the rhizosphere, and those positive interactions progressively dominated the co-occurrence network along the soil-rhizosphere-root continuum. Collectively, root niches dominantly affected the root-associated microbiome and the positive interkingdom interactions increased, potentially providing benefits for the blueberry.

Pseudomonas ability to utilize different carbon substrates and adaptation influenced by protozoan grazing

Bacteria are major utilizers of dissolved organic matter in aquatic systems. In coastal areas bacteria are supplied with a mixture of food sources, spanning from refractive terrestrial dissolved organic matter to labile marine autochthonous organic matter. Modelling scenarios indicate that in northern coastal areas, the inflow of terrestrial organic matter will increase, and autochthonous production will decrease, thus bacteria will experience a change in the food source composition. How bacteria will cope with such changes is not known. Here, we tested the ability of an isolated bacterium from the northern Baltic Sea coast, Pseudomonas sp., to adapt to varying substrates. We performed a 7-months chemostat experiment, where three different substrates were provided: glucose, representing labile autochthonous organic carbon, sodium benzoate representing refractive organic matter, and acetate - a labile but low energy food source. Growth rate has been pointed out as a key factor for fast adaptation, and since protozoan grazers speed-up the growth rate we added a ciliate to half of the incubations. The results show that the isolated Pseudomonas is adapted to utilize both labile and ring-structured refractive substrates. The growth rate was the highest on the benzoate substrate, and the production increased over time indicating that adaptation did occur. Further, our findings indicate that predation can cause Pseudomonas to change their phenotype to resist and promote survival in various carbon substrates. Genome sequencing reveals different mutations in the genome of adapted populations compared to the native populations, suggesting the adaptation of Pseudomonas sp. To changing environment.

Bacterial defences: mechanisms, evolution and antimicrobial resistance

Throughout their evolutionary history, bacteria have faced diverse threats from other microorganisms, including competing bacteria, bacteriophages and predators. In response to these threats, they have evolved sophisticated defence mechanisms that today also protect bacteria against antibiotics and other therapies. In this Review, we explore the protective strategies of bacteria, including the mechanisms, evolution and clinical implications of these ancient defences. We also review the countermeasures that attackers have evolved to overcome bacterial defences. We argue that understanding how bacteria defend themselves in nature is important for the development of new therapies and for minimizing resistance evolution.

Legionella pneumophila and Free-Living Nematodes: Environmental Co-Occurrence and Trophic Link

Free-living nematodes harbor and disseminate various soil-borne bacterial pathogens. Whether they function as vectors or environmental reservoirs for the aquatic L. pneumophila, the causative agent of Legionnaires’ disease, is unknown. A survey screening of biofilms of natural (swimming lakes) and technical (cooling towers) water habitats in Germany revealed that nematodes can act as potential reservoirs, vectors or grazers of L. pneumophila in cooling towers. Consequently, the nematode species Plectus similis and L. pneumophila were isolated from the same cooling tower biofilm and taken into a monoxenic culture. Using pharyngeal pumping assays, potential feeding relationships between P. similis and different L. pneumophila strains and mutants were examined and compared with Plectus sp., a species isolated from a L. pneumophila-positive thermal source biofilm. The assays showed that bacterial suspensions and supernatants of the L. pneumophila cooling tower isolate KV02 decreased pumping rate and feeding activity in nematodes. However, assays investigating the hypothesized negative impact of Legionella’s major secretory protein ProA on pumping rate revealed opposite effects on nematodes, which points to a species-specific response to ProA. To extend the food chain by a further trophic level, Acanthamoebae castellanii infected with L. pneumphila KV02 were offered to nematodes. The pumping rates of P. similis increased when fed with L. pneumophila-infected A. castellanii, while Plectus sp. pumping rates were similar when fed either infected or non-infected A. castellanii. This study revealed that cooling towers are the main water bodies where L. pneumophila and free-living nematodes coexist and is the first step in elucidating the trophic links between coexisting taxa from that habitat. Investigating the Legionella–nematode–amoebae interactions underlined the importance of amoebae as reservoirs and transmission vehicles of the pathogen for nematode predators.

Shifts from cooperative to individual-based predation defense determine microbial predator-prey dynamics

Predation defense is an important feature of predator-prey interactions adding complexity to ecosystem dynamics. Prey organisms have developed various strategies to escape predation which differ in mode (elude vs. attack), reversibility (inducible vs. permanent), and scope (individual vs. cooperative defenses). While the mechanisms and controls of many singular defenses are well understood, important ecological and evolutionary facets impacting long-term predator-prey dynamics remain underexplored. This pertains especially to trade-offs and interactions between alternative defenses occurring in prey populations evolving under predation pressure. Here, we explored the dynamics of a microbial predator-prey system consisting of bacterivorous flagellates (Poteriospumella lacustris) feeding on Pseudomonas putida. Within five weeks of co-cultivation corresponding to about 35 predator generations, we observed a consistent succession of bacterial defenses in all replicates (n = 16). Initially, bacteria expressed a highly effective cooperative defense based on toxic metabolites, which brought predators close to extinction. This initial strategy, however, was consistently superseded by a second mechanism of predation defense emerging via de novo mutations. Combining experiments with mathematical modeling, we demonstrate how this succession of defenses is driven by the maximization of individual rather than population benefits, highlighting the role of rapid evolution in the breakdown of social cooperation.

Multiple Receptors Contribute to the Attractive Response of Caenorhabditis elegans to Pathogenic Bacteria

Nematodes feed mainly on bacteria and sense volatile signals through their chemosensory system to distinguish food from pathogens. Although nematodes recognizing bacteria by volatile metabolites are ubiquitous, little is known of the associated molecular mechanism. Here, we show that the antinematode bacterium Paenibacillus polymyxa KM2501-1 exhibits an attractive effect on Caenorhabditis elegans via volatile metabolites, of which furfural acetone (FAc) acts as a broad-spectrum nematode attractant. We show that the attractive response toward FAc requires both the G-protein-coupled receptors STR-2 in AWC neurons and SRA-13 in AWA and AWC neurons. In the downstream olfactory signaling cascades, both the transient receptor potential vanilloid channel and the cyclic nucleotide-gated channel are necessary for FAc sensation. These results indicate that multiple receptors and subsequent signaling cascades contribute to the attractive response of C. elegans to FAc, and FAc is the first reported ligand of SRA-13. Our current work discovers that P. polymyxa KM2501-1 exhibits an attractive effect on nematodes by secreting volatile metabolites, especially FAc and 2-heptanone, broadening our understanding of the interactions between bacterial pathogens and nematodes. IMPORTANCE Nematodes feed on nontoxic bacteria as a food resource and avoid toxic bacteria; they distinguish them through their volatile metabolites. However, the mechanism of how nematodes recognize bacteria by volatile metabolites is not fully understood. Here, the antinematode bacterium Paenibacillus polymyxa KM2501-1 is found to exhibit an attractive effect on Caenorhabditis elegans via volatile metabolites, including FAc. We further reveal that the attractive response of C. elegans toward FAc requires multiple G-protein-coupled receptors and downstream olfactory signaling cascades in AWA and AWC neurons. This study highlights the important role of volatile metabolites in the interaction between nematodes and bacteria and confirms that multiple G-protein-coupled receptors on different olfactory neurons of C. elegans can jointly sense bacterial volatile signals.

The potential of facultative predatory Actinomycetota spp. and prospects in agricultural sustainability

Actinomycetota in the phylum of bacteria has been explored extensively as a source of antibiotics and secondary metabolites. In addition to acting as plant growth-promoting agents, they also possess the potential to control various plant pathogens; however, there are limited studies that report the facultative predatory ability of Actinomycetota spp. Furthermore, the mechanisms that underline predation are poorly understood. We assessed the diversity of strategies employed by predatory bacteria to attack and subsequently induce the cell lysing of their prey. We revisited the diversity and abundance of secondary metabolite molecules linked to the different predation strategies by bacteria species. We analyzed the pros and cons of the distinctive predation mechanisms and explored their potential for the development of new biocontrol agents. The facultative predatory behaviors diverge from group attack "wolfpack," cell-to-cell proximity "epibiotic," periplasmic penetration, and endobiotic invasion to degrade host-cellular content. The epibiotic represents the dominant facultative mode of predation, irrespective of the habitat origins. The wolfpack is the second-used approach among the Actinomycetota harboring predatory traits. The secondary molecules as chemical weapons engaged in the respective attacks were reviewed. We finally explored the use of predatory Actinomycetota as a new cost-effective and sustainable biocontrol agent against plant pathogens.

What Drives the Assembly of Plant-associated Protist Microbiomes? Investigating the Effects of Crop Species, Soil Type and Bacterial Microbiomes

In a field experiment we investigated the influence of the environmental filters soil type (i.e. three contrasting soils) and plant species (i.e. lettuce and potato) identity on rhizosphere community assembly of Cercozoa, a dominant group of mostly bacterivorous soil protists. Plant species (14%) and rhizosphere origin (vs bulk soil) with 13%, together explained four times more variation in cercozoan beta diversity than the three soil types (7% explained variation). Our results clearly confirm the existence of plant species-specific protist communities. Network analyses of bacteria-Cercozoa rhizosphere communities identified scale-free small world topologies, indicating mechanisms of self-organization. While the assembly of rhizosphere bacterial communities is bottom-up controlled through the resource supply from root (secondary) metabolites, our results support the hypothesis that the net effect may depend on the strength of top-down control by protist grazers. Since grazing of protists has a strong impact on the composition and functioning of bacteria communities, protists expand the repertoire of plant genes by functional traits, and should be considered as 'protist microbiomes' in analogy to 'bacterial microbiomes'.

Comparative transcriptome combined with morphophysiological analyses revealed the molecular mechanism underlying Tetrahymena thermophila predation-induced antiphage defense in Aeromonas hydrophila

Protozoan predation has been demonstrated to be a strong driving force for bacterial defence strategies in the environment. Our previous study demonstrated that Aeromonas hydrophila NJ-35, which evolved small-colony variants (SCVs), displayed various adaptive traits in response to Tetrahymena thermophila predation, such as enhanced phage resistance. However, the evolutionary mechanisms are largely unknown. In this study, we performed a genome- and transcriptome-wide analysis of the SCV1, representing one strain of the SCVs, for identification of the genes of mutation and altered expression underlying this phage resistance phenotype. Our study demonstrated that phage resistance caused by T. thermophila predation was due to the downregulation of a flagellar biosynthesis regulator, flhF, in SCV1. Interestingly, we confirmed that phage resistance in SCV1 was not straightforwardly attributable to the absence of flagella but to FlhF-mediated secretion of extracellular protein that hinders phage adsorption. This finding improves our understanding of the mechanisms by which A. hydrophila lowers the susceptibility to phage infection under predation pressure, and highlights an important contribution of bacterium–protozoan interactions in driving the adaptive evolution of pathogens in complex environments.

Interaction of Talaromyces marneffei with free living soil amoeba as a model of fungal pathogenesis

Talaromyces (Penicillium) marneffei is an important dimorphic mycosis endemic in Southeast Asia and Southern China, but the origin and maintenance of virulence traits in this organism remains obscure. Several pathogenic fungi, including Cryptococcus neoformans, Aspergillus fumigatus, Blastomyces dermatitidis, Sporothrix schenckii, Histoplasma capsulatum and Paracoccidioides spp. interact with free living soil amoebae and data suggests that fungal pathogenic strategies may emerge from environmental interactions of these fungi with ubiquitous phagocytic microorganisms. In this study, we examined the interactions of T. marneffei with the soil amoeba Acanthamoeba castellanii. T. marneffei was rapidly ingested by A. castellanii and phagocytosis of fungal cells resulted in amoeba death after 24 h of contact. Co-culture also resulted in a rapid transition for conidia to the fission-yeast form. In addition, well-established virulence factors such as melanin and a yeast specific mannoprotein of T. marneffei were expressed during interaction with A. castellanii at 37°C. Our findings support the assumption that soil amoebae environmental predators play a role in the selection and maintenance of particular features in T. marneffei that impart virulence to this clinically important dimorphic fungus in mammalian hosts.

Intermediate Levels of Predation and Nutrient Enrichment Enhance the Activity of Ibuprofen-Degrading Bacteria

Water is the most indispensable natural resource; yet, organic pollution of freshwater sources is widespread. In recent years, there has been increasing concern over the vast array of emerging organic contaminants (EOCs) in the effluent of wastewater treatment plants (WWTPs). Several of these EOCs are degraded within the pore space of riverbeds by active microbial consortia. However, the mechanisms behind this ecosystem service are largely unknown. Here, we report how phosphate concentration and predator-prey interactions drive the capacity of bacteria to process a model EOC (ibuprofen). The presence of phosphate had a significant positive effect on the population growth rate of an ibuprofen-degrading strain. Thus, when phosphate was present, ibuprofen removal efficiency increased. Moreover, low and medium levels of predation, by a ciliated protozoan, stimulated bacterial population growth. This unimodal effect of predation was lost under high phosphate concentration, resulting in the flattening of the relationships between predator density and population growth of ibuprofen degraders. Our results suggest that moderate nutrient and predation levels promote the growth rate of bacterial degraders and, consequently, the self-purifying capability of the system. These findings enhance our understanding of the mechanisms by which riverbed communities drive the processing of EOCs.

Trade-offs of lipid remodeling in a marine predator-prey interaction in response to phosphorus limitation

Microbial growth is often limited by key nutrients like phosphorus (P) across the global ocean. A major response to P limitation is the replacement of membrane phospholipids with non-P lipids to reduce their cellular P quota. However, the biological “costs” of lipid remodeling are largely unknown. Here, we uncover a predator–prey interaction trade-off whereby a lipid-remodeled bacterial prey cell becomes more susceptible to digestion by a protozoan predator facilitating its rapid growth. Thus, we highlight a complex interplay between adaptation to the abiotic environment and consequences for biotic interactions (grazing), which may have important implications for the stability and structuring of microbial communities and the performance of the marine food web.

Phosphorus (P) is a key nutrient limiting bacterial growth and primary production in the oceans. Unsurprisingly, marine microbes have evolved sophisticated strategies to adapt to P limitation, one of which involves the remodeling of membrane lipids by replacing phospholipids with non-P-containing surrogate lipids. This strategy is adopted by both cosmopolitan marine phytoplankton and heterotrophic bacteria and serves to reduce the cellular P quota. However, little, if anything, is known of the biological consequences of lipid remodeling. Here, using the marine bacterium Phaeobacter sp. MED193 and the ciliate Uronema marinum as a model, we sought to assess the effect of remodeling on bacteria–protist interactions. We discovered an important trade-off between either escape from ingestion or resistance to digestion. Thus, Phaeobacter grown under P-replete conditions was readily ingested by Uronema, but not easily digested, supporting only limited predator growth. In contrast, following membrane lipid remodeling in response to P depletion, Phaeobacter was less likely to be captured by Uronema, thanks to the reduced expression of mannosylated glycoconjugates. However, once ingested, membrane-remodeled cells were unable to prevent phagosome acidification, became more susceptible to digestion, and, as such, allowed rapid growth of the ciliate predator. This trade-off between adapting to a P-limited environment and susceptibility to protist grazing suggests the more efficient removal of low-P prey that potentially has important implications for the functioning of the marine microbial food web in terms of trophic energy transfer and nutrient export efficiency.

Land use alters diazotroph community structure by regulating bacterivores in Mollisols in Northeast China

Changes in land use can generate environmental pressures that influence soil biodiversity, and numerous studies have examined the influences of land use on the soil microbial communities. However, little is known about the effects of land use on ecological interactions of soil microbes and their predators. Diazotrophs are key soil microbes that play important functional roles in fixing atmospheric nitrogen. In this study, we investigated the co-association of diazotroph community members and patterns of diazotroph and bacterivore networks under different long-term land uses including cropland, grassland, and bare land. Diazotroph community was characterized by high-throughput sequencing. The results indicated that land use type influenced the dominant genera of diazotrophs and shaped the occurrence of specific indicator diazotroph taxa. Co-existing pattern analysis of diazotrophs and bacterivores indicated that grassland converted from cropland increased the complexity of diazotroph and bacterivore network structure. The number of nodes for diazotrophs and bacterivores was higher in grassland than in cropland and bare land. Random forest analysis revealed that six bacterivore genera Cephalobus, Protorhabditis, Acrobeloides, Mesorhabditis, Anaplectus, and Monhystera had significant effects on diazotrophs. Bacterivores were found to have predominantly negative effects in bare land. Different bacterivores had differing effects with respect to driving changes in diazotroph community structure. Structural equation model showed that land use could control diazotroph community composition by altering soil properties and regulating abundance of bacterivores. These findings accordingly enhance our current understanding of mechanisms underlying the influence of land use patterns on diazotrophs from the perspective of soil food webs.

Identification and feeding characteristics of the mixotrophic flagellate Poterioochromonas malhamensis, a microalgal predator isolated from planting water of Pontederia cordata

The microorganisms and allelochemicals in Pontederia cordata planting water may have a synergistic inhibitory effect on algae. To study this synergy, an algae-inhibiting organism was isolated and identified, and its growth and feeding characteristics were studied. The organism was identified as Poterioochromonas malhamensis yzs924 based on both its morphology and molecular barcoding employing 18S rDNA gene sequences.The growth and feeding of P. malhamensis were affected by environmental factors and the state of its prey. (1) P. malhamensis is a mixotrophic flagellate. Its heterotrophic growth was the fastest in a wheat grain medium, and its growth rate in this study reached 2.5 day^-1. (2) Within a short period of time (2 days), P. malhamensis growth was slower under continuous dark conditions than under alternating light and dark conditions, but it fed on Microcystis aeruginosa more rapidly under dark conditions. (3) High pH was disadvantageous to the growth and grazing of P. malhamensis. When the pH was kept stable at 9, P. malhamensis could not grow continuously. (4) When the initial density of M. aeruginosa was 5 × 10⁷ cells/mL or is in a period of decline, P. malhamensis could not remove all M. aeruginosa. The combined use of P. malhamensis and allelochemicals may represent a method of M. aeruginosa control, but this approach requires further research.

Faunal communities mediate the effects of plant richness, drought, and invasion on ecosystem multifunctional stability

Understanding the stability of ecosystem multifunctionality is imperative for maintaining ecosystem health and sustainability under augmented global change. However it remains unknown whether and how biological communities mediate multifunctional stability in response to biodiversity loss and disturbances. Here, we conducted a 3-year experiment by exposing 270 plant communities of four plant richness levels, i.e., 1, 2, 4, or 8 species, to drought and exotic plant invasion disturbances. Then, the direct effects of plant richness, drought and invasion, and their indirect effects mediated by the stability of plant, litter-faunal, and soil-faunal communities on multifunctional stability were disentangled. We found that plant richness increased, while drought and invasion decreased ecosystem multifunctional stability, which were mediated by plant or faunal community stability. By incorporating the stability of communities into the complex ecological mechanisms, the completeness and goodness of ecological models for explaining and maintaining the stability of ecosystem multifunctionality will be improved.

Response of Prokaryotic Communities to Freshwater Salinization

Each year, millions of tons of sodium chloride are dumped on roads, contributing to the salinization of freshwater environments. Thus, we sought to understand the effect of sodium chloride (NaCl) on freshwater lake prokaryotic communities, an important and understudied component of food webs. Using mesocosms with 0.01–2.74 ppt NaCl (0.27–1110.86 mg/L Cl−), we evaluated the effect generated on the diversity and absolute abundance of prokaryotic populations after three and six weeks. A positive relationship between Cl− values and absolute bacterial abundance was found after three weeks. The influence of eukaryotic diversity variation was observed as well. Significant differentiation of bacterial communities starting at 420 mg/L Cl− was observed after three weeks, levels lower than the Canadian and US recommendations for acute chloride exposure. The partial recovery of a “pre-disturbance” community was observed following a drop in salinity at the threshold level of 420 mg/L Cl−. A gradual transition of dominance from Betaproteobacteria and Actinobacteria to Bacteroidia and Alphaproteobacteria was observed and is overall similar to the natural transition observed in estuaries.

Protist feeding patterns and growth rate are related to their predatory impacts on soil bacterial communities

Predatory protists are major consumers of soil micro-organisms. By selectively feeding on their prey, they can shape soil microbiome composition and functions. While different protists are known to show diverging impacts, it remains impossible to predict a priori the effect of a given species. Various protist traits including phylogenetic distance, growth rate and volume have been previously linked to the predatory impact of protists. Closely-related protists,however, also showed distinct prey choices which could mirror specificity in their dietary niche. We, therefore, aimed to estimate the dietary niche breadth and overlap of eight protist isolates on 20 bacterial species in plate assays. To assess the informative value of previously suggested and newly proposed (feeding-related) protist traits, we related them to the impacts of predation of each protist on a protist-free soil bacterial community in a soil microcosm via 16S rRNA gene amplicon sequencing. We could demonstrate that each protist showed a distinct feeding pattern in vitro. Further, the assayed protist feeding patterns and growth rates correlated well with the observed predatory impacts on the structure of soil bacterial communities. We thus conclude that in vitro screening has the potential to inform on the specific predatory impact of selected protists.

Current status of microbes involved in the degradation of pharmaceutical and personal care products (PPCPs) pollutants in the aquatic ecosystem

Contamination of aquatic systems with pharmaceuticals, personal care products, steroid hormones, and agrochemicals has been an immense problem for the earth's ecosystem and health impacts. The environmental issues of well-known persistence pollutants, their metabolites, and other micro-pollutants in diverse aquatic systems around the world were collated and exposed in this review assessment. Waste Water Treatment Plant (WWTP) influents and effluents, as well as industrial, hospital, and residential effluents, include detectable concentrations of known and undiscovered persistence pollutants and metabolites. These components have been found in surface water, groundwater, drinking water, and natural water reservoirs receiving treated and untreated effluents. Several studies have found that these persistence pollutants, and also similar recalcitrant pollutants, are hazardous to a variety of non-targeted creatures in the environment. In human and animals, they can also have severe and persistent harmful consequences. Because these pollutants are harmful to aquatic organisms, microbial degradation of these persistence pollutants had the least efficiency. Fortunately, only a few wild and Genetically Modified (GMOs) microbial species have the ability to degrade these PPCPs contaminants. Hence, researchers have been studying the degradation competence of microbial communities in persistence pollutants of Pharmaceutical and Personal Care Products (PPCPs) and respective metabolites for decades, as well as possible degradation processes in various aquatic systems. As a result, this review provides comprehensive information about environmental issues and the degradation of PPCPs and their metabolites, as well as other micro-pollutants, in aquatic systems.

Symbiont-Induced Phagosome Changes Rather than Extracellular Discrimination Contribute to the Formation of Social Amoeba Farming Symbiosis

Symbiont recognition is essential in many symbiotic relationships, especially for horizontally transferred symbionts. Therefore, how to find the right partner is a crucial challenge in these symbiotic relationships. Previous studies have demonstrated that both animals and plants have evolved various mechanisms to recognize their symbionts. However, studies about the mechanistic basis of establishing protist-bacterium symbioses are scarce. This study investigated this question using a social amoeba Dictyostelium discoideum and their Burkholderia symbionts. We found no evidence that D. discoideum hosts could distinguish different Burkholderia extracellularly in chemotaxis assays. Instead, symbiont-induced phagosome biogenesis contributed to the formation of social amoeba symbiosis, and D. discoideum hosts have a higher phagosome pH when carrying symbiotic Burkholderia than nonsymbiotic Burkholderia. In conclusion, the establishment of social amoeba symbiosis is not linked with extracellular discrimination but related to symbiont-induced phagosome biogenesis, which provides new insights into the mechanisms of endosymbiosis formation between protists and their symbionts.

IMPORTANCE Protists are single-celled, extremely diverse eukaryotic microbes. Like animals and plants, they live with bacterial symbionts and have complex relationships. In protist-bacterium symbiosis, while some symbionts are strictly vertically transmitted, others need to reestablish and acquire symbionts from the environment frequently. However, the mechanistic basis of establishing protist-bacterium symbioses is mostly unclear. This study uses a novel amoeba-symbiont system to show that the establishment of this symbiosis is not linked with extracellular discrimination. Instead, symbiont-induced phagosome biogenesis contributes to the formation of social amoeba-bacterium symbiosis. This study increases our understanding of the mechanistic basis of establishing protist-bacterium symbioses.

Adaptation and phenotypic diversification of Bacillus thuringiensis biofilm are accompanied by fuzzy spreader morphotypes

Bacillus cereus group (Bacillus cereus sensu lato) has a diverse ecology, including various species that produce biofilms on abiotic and biotic surfaces. While genetic and morphological diversification enables the adaptation of multicellular communities, this area remains largely unknown in the Bacillus cereus group. In this work, we dissected the experimental evolution of Bacillus thuringiensis 407 Cry- during continuous recolonization of plastic beads. We observed the evolution of a distinct colony morphotype that we named fuzzy spreader (FS) variant. Most multicellular traits of the FS variant displayed higher competitive ability versus the ancestral strain, suggesting an important role for diversification in the adaptation of B. thuringiensis to the biofilm lifestyle. Further genetic characterization of FS variant revealed the disruption of a guanylyltransferase gene by an insertion sequence (IS) element, which could be similarly observed in the genome of a natural isolate. The evolved FS and the deletion mutant in the guanylyltransferase gene (Bt407ΔrfbM) displayed similarly altered aggregation and hydrophobicity compared to the ancestor strain, suggesting that the adaptation process highly depends on the physical adhesive forces.

The Ubiquitous Soil Terpene Geosmin Acts as a Warning Chemical

Known as the smell of earth after rain, geosmin is an odorous terpene detectable by humans at picomolar concentrations. Geosmin production is heavily conserved in actinobacteria, myxobacteria, cyanobacteria, and some fungi, but its biological activity is poorly understood. We theorized that geosmin was an aposematic signal used to indicate the unpalatability of toxin-producing microbes, discouraging predation by eukaryotes. Consistent with this hypothesis, we found that geosmin altered the behavior of the bacteriophagous nematode Caenorhabditis elegans on agar plates in the absence of bacteria. Normal movement was restored in mutant worms lacking differentiated ASE (amphid neurons, single ciliated endings) neurons, suggesting that geosmin is a taste detected by the nematodal gustatory system. In a predation assay, geosmin and the related terpene 2-methylisoborneol reduced grazing on the bacterium Streptomyces coelicolor. Predation was restored by the removal of both terpene biosynthetic pathways or the introduction of C. elegans that lacked differentiated ASE taste neurons, leading to the apparent death of both bacteria and worms. While geosmin and 2-methylisoborneol appeared to be nontoxic, grazing triggered bacterial sporulation and the production of actinorhodin, a pigment coproduced with a number of toxic metabolites. In this system, geosmin thus appears to act as a warning signal indicating the unpalatability of its producers and reducing predation in a manner that benefits predator and prey. This suggests that molecular signaling may affect microbial predator-prey interactions in a manner similar to that of the well-studied visual markers of poisonous animal prey. IMPORTANCE One of the key chemicals that give soil its earthy aroma, geosmin is a frequent water contaminant produced by a range of unrelated microbes. Many animals, including humans, are able to detect geosmin at minute concentrations, but the benefit that this compound provides to its producing organisms is poorly understood. We found that geosmin repelled the bacterial predator Caenorhabditis elegans in the absence of bacteria and reduced contact between the worms and the geosmin-producing bacterium Streptomyces coelicolor in a predation assay. While geosmin itself appears to be nontoxic to C. elegans, these bacteria make a wide range of toxic metabolites, and grazing on them harmed the worms. In this system, geosmin thus appears to indicate unpalatable bacteria, reducing predation and benefiting both predator and prey. Aposematic signals are well known in animals, and this work suggests that metabolites may play a similar role in the microbial world.

Precipitous Increase of Bacterial CRISPR-Cas Abundance at Around 45°C

Although performing adaptive immunity, CRISPR-Cas systems are present in only 40% of bacterial genomes. We observed an abrupt increase of bacterial CRISPR-Cas abundance at around 45°C. Phylogenetic comparative analyses confirmed that the abundance correlates with growth temperature only at the temperature range around 45°C. From the literature, we noticed that the diversities of cellular predators (like protozoa, nematodes, and myxobacteria) have a steep decline at this temperature range. The grazing risk faced by bacteria reduces substantially at around 45°C and almost disappears above 60°C. We propose that viral lysis would become the dominating factor of bacterial mortality, and antivirus immunity has a higher priority at higher temperatures. In temperature ranges where the abundance of cellular predators does not change with temperature, the growth temperatures of bacteria would not significantly affect their CRISPR-Cas contents. The hypothesis predicts that bacteria should also be rich in CRISPR-Cas systems if they live in other extreme conditions inaccessible to grazing predators.

Selective drivers of simple multicellularity

In order to understand the evolution of multicellularity, we must understand how and why selection favors the first steps in this process: the evolution of simple multicellular groups. Multicellularity has evolved many times in independent lineages with fundamentally different ecologies, yet no work has yet systematically examined these diverse selective drivers. Here we review recent developments in systematics, comparative biology, paleontology, synthetic biology, theory, and experimental evolution, highlighting ten selective drivers of simple multicellularity. Our survey highlights the many ecological opportunities available for simple multicellularity, and stresses the need for additional work examining how these first steps impact the subsequent evolution of complex multicellularity.

Contrasting effects of soil microbial interactions on growth-defence relationships between early- and mid-successional plant communities

Plants allocate resources to processes related to growth and enemy defence. Simultaneously, they interact with complex soil microbiomes that also affect plant performance. While the influence of individual microbial groups on single plants is increasingly studied, effects of microbial interactions on growth, defence and growth-defence relationships remain unknown, especially at the plant community level. We investigated how three microbial groups (bacteria, fungi, protists), alone and in full-factorial combinations, affect plant performance and potential growth-defence relationships by measuring phenolics composition in early- and mid-successional grass and forb communities in a glasshouse experiment. Microbial groups did not affect plant growth and only fungi increased defence compounds in early- and mid-successional forbs, while grasses were not affected. Shoot biomass-defence relationships were negatively correlated in most microbial treatments in early-successional forbs, but positively in several microbial treatments in mid-successional forbs. The growth-defence relationship was generally negative in early-successional but not in mid-successional grasses. The presence of different microbiomes commonly removed the observed growth-defence relationships. We conclude that soil microorganisms and their interactions can shift growth-defence relationships differentially for plant functional groups and the relationships vary between successional stages. Microbial interaction-induced growth-defence shifts might therefore underlie distinct plant strategies and fitness.

Nematodes as Ghosts of Land Use Past: Elucidating the Roles of Soil Nematode Community Studies as Indicators of Soil Health and Land Management Practices

Soil health is a matter of growing concern because of its degradation due to unsustainable anthropogenic activities over the last few decades. It is maintained by interactions among the components of the soil food web commonly concentrated in the vicinity of the plant roots, called the rhizosphere. The soil food web is dominated by nematodes. They occupy various trophic positions because of their diverse feeding habits. The free-living forms are mainly dependent on soil bacteria and fungi for their nutrition, while the parasitic forms feed on plant roots. The population of these two groups is regulated by the activities of predatory nematodes which can be carnivorous or omnivorous. The soil nematodes thereby partake responsibilities in nutrient cycling, mineralization and decomposition pathways which, in turn, affects the aboveground productivity. This intricately connected food web structure is vulnerable to disturbances like increased soil salinity, acidity, nitrogen enrichment, tillage, crop rotations, fertilizers, pesticides, soil amendment techniques and heavy metal pollution. The effects are reflected by alterations in the abundance and diversity of soil nematodes belonging to various trophic groups. These alterations have been formulated into measurable indices like maturity index (MI), structure index (SI), enrichment index (EI) and channel index (CI). The faunal profile and metabolic footprints of soil nematodes are latest developments in the field of nematode community analyses. Though these indices cannot replace the conventional soil ecotoxicological assays, they can give added information about soil biology which can be utilized to design sustainable land use practices.

Identifying Edaphic Factors and Normalized Difference Vegetation Index Metrics Driving Wildlife Mortality From Anthrax in Kenya’s Wildlife Areas

Anthrax, an acute disease of homeotherms caused by soil-borne Bacillus anthracis is implicated in dramatic declines in wildlife mainly in sub-Saharan Africa. Anthrax outbreaks are often localized in space and time. Therefore, understanding predictors of the spatial and temporal occurrence of anthrax in wildlife areas is useful in supporting early warning and improved response and targeting measures to reduce the impact of epizootic risk on populations. Spatial localization of anthrax is hypothesized to be driven by edaphic factors, while the temporal outbreaks are thought to be driven by extreme weather events including temperature, humidity, rainfall, and drought. Here, we test the role of select edaphic factors and normalized difference vegetation index (NDVI) metrics driven by vegetation structure and climate variability on the spatial and temporal patterns of wildlife mortality from anthrax in key wildlife areas in Kenya over a 20-year period, from 2000 to 2019. There was a positive association between the number of anthrax outbreaks and the total number of months anthrax was reported during the study period and the nitrogen and organic carbon content of the soil in each wildlife area. The monthly occurrence (timing) of anthrax in Lake Nakuru (with the most intense outbreaks) was positively related to the previous month’s spatial heterogeneity in NDVI and monthly NDVI deviation from 20-year monthly means. Generalized linear models revealed that the number of months anthrax was reported in a year (intensity) was positively related to spatial heterogeneity in NDVI, total organic carbon and cation exchange capacity of the soil. These results, examined in the light of experimental studies on anthrax persistence and amplification in the soil enlighten on mechanisms by which these factors are driving anthrax outbreaks and spatial localization.

Consumers' active choice behaviour promotes coevolutionary units in antagonistic networks

Individual behaviour and local context can influence the evolution of ecological interactions and how they structure into networks. In trophic interactions, consumers can increase their fitness by actively choosing resources that they are more likely to explore successfully. Mathematical modelling is often employed in theoretical studies to understand the coevolutionary dynamics between consumers and resources. However, they often disregard the individual consumer behaviour since the complexity of these systems usually requires simplifying assumptions about interaction details. Using an individual-based model, we model a community of several species that interact antagonistically. Each individual has a trait (attack or defence) that is explicitly modelled and the probability of the interaction to occur successfully increases with increased trait-matching. In addition, consumers can actively choose resources that guarantee greater fitness. We show that active consumer choice can generate coevolutionary units over time. It means that the traits of both consumers and resources converge into multiple groups with similar traits and the species interactions stay restricted to these groups over time. We also observed that network structure is more dependent on the parameter that delimits active consumer choice than on the intensity of selective pressure. Thus, our results support the idea that consumer active choice behaviour plays an important role in the ecological and evolutionary processes that structure interacting communities.

Loss of the acetate switch in Vibrio vulnificus enhances predation defence against Tetrahymena pyriformis

Vibrio vulnificus is an opportunistic human pathogen and autochthonous inhabitant of coastal marine environments, where the bacterium is under constant predation by heterotrophic protists or protozoans. As a result of this selection pressure, genetic variants with antipredation mechanisms are selected for and persist in the environment. Such natural variants may also be pathogenic to animal or human hosts, making it important to understand these defense mechanisms. To identify antipredator strategies, 13 V. vulnificus strains of different genotypes isolated from diverse environments were exposed to predation by the ciliated protozoan Tetrahymena pyriformis, and only strain ENV1 was resistant to predation. Further investigation of the cell-free supernatant showed that ENV1 acidifies the environment by the excretion of organic acids, which are toxic to T. pyriformis. As this predation resistance was dependent on the availability of iron, transcriptomes of V. vulnificus in iron-replete and iron-deplete conditions were compared. This analysis revealed that ENV1 ferments pyruvate and the resultant acetyl-CoA leads to acetate synthesis under aerobic conditions, a hallmark of overflow metabolism. The anaerobic respiration global regulator arcA was upregulated when iron was available. An ΔarcA deletion mutant of ENV1 accumulated less acetate and, importantly, was sensitive to grazing by T. pyriformis. Based on the transcriptome response and quantification of metabolites, we conclude that ENV1 has adapted to overflow metabolism and has lost a control switch that shifts metabolism from acetate excretion to acetate assimilation, enabling it to excrete acetate continuously. We show that overflow metabolism and the acetate switch contribute to prey-predator interactions.

IMPORTANCE Bacteria in the environment, including Vibrio spp., interact with protozoan predators. To defend against predation, bacteria evolve antipredator mechanisms ranging from changing morphology, biofilm formation, and secretion of toxins or virulence factors. Some of these adaptations may result in strains that are pathogenic to humans. Therefore, it is important to study predator defense strategies of environmental bacteria. V. vulnificus thrives in coastal waters and infects humans. Very little is known about the defense mechanisms V. vulnificus expresses against predation. Here, we show that a V. vulnificus strain (ENV1) has rewired the central carbon metabolism, enabling the production of excess organic acid that is toxic to the protozoan predator T. pyriformis. This is a previously unknown mechanism of predation defense that protects against protozoan predators.

Specialized Metabolite Mediated Predation Defense in the Marine Actinobacterium Salinispora

The obligate marine actinobacterial genus Salinispora has become a model organism for natural product discovery, yet little is known about the ecological functions of the compounds produced by this taxon. The aims of this study were to assess the effects of live cultures and culture extracts from two Salinispora species on invertebrate predators. In choice-based feeding experiments using the bacterivorous nematode Caenorhabditis elegans, live cultures of both Salinispora species were less preferred than E. coli. When given a choice between the two species, C. elegans preferred S. areniolca over S. tropica. Culture extracts from S. tropica deterred C. elegans while those from S. arenicola did not, suggesting that compounds produced by S. tropica may account for the feeding deterrence. Bioactivity guided isolation linked compounds in the lomaiviticin series to the deterrent activity. Additional assays using the marine polychaete Ophryotrocha siberti and marine nematodes further support the deterrent activity of S. tropica against potential predators. These results provide evidence that Salinispora natural products may function as a defense against predation and that the strategies of predation defense differ between closely related species. Importance Bacteria inhabiting marine sediments are subject to predation by bacterivorous eukaryotes. Here we test the hypothesis that sediment-derived bacteria in the genus Salinispora produce biologically active natural products that function as a defense against predation. The results reveal that cultures and culture extracts of S. tropica deter feeding by Caenorhabditis elegans and negatively affect the habitat preference of a marine annelid (Ophryotrocha siberti). These activities were linked to the lomaiviticins, a series of cytotoxic compounds produced by S. tropica. Microbial natural products that function as a defense against predation represent a poorly understood trait that can influence community structure in marine sediments.

Predatory Bacteria Select for Sustained Prey Diversity

Predator impacts on prey diversity are often studied among higher organisms over short periods, but microbial predator-prey systems allow examination of prey-diversity dynamics over evolutionary timescales. We previously showed that Escherichia coli commonly evolved minority mucoid phenotypes in response to predation by the bacterial predator Myxococcus xanthus by one time point of a coevolution experiment now named MyxoEE-6. Here we examine mucoid frequencies across several MyxoEE-6 timepoints to discriminate between the hypotheses that mucoids were increasing to fixation, stabilizing around equilibrium frequencies, or heading to loss toward the end of MyxoEE-6. In four focal coevolved prey populations, mucoids rose rapidly early in the experiment and then fluctuated within detectable minority frequency ranges through the end of MyxoEE-6, generating frequency dynamics suggestive of negative frequency-dependent selection. However, a competition experiment between mucoid and non-mucoid clones found a predation-specific advantage of the mucoid clone that was insensitive to frequency over the examined range, leaving the mechanism that maintains minority mucoidy unresolved. The advantage of mucoidy under predation was found to be associated with reduced population size after growth (productivity) in the absence of predators, suggesting a tradeoff between productivity and resistance to predation that we hypothesize may reverse mucoid vs non-mucoid fitness ranks within each MyxoEE-6 cycle. We also found that mucoidy was associated with diverse colony phenotypes and diverse candidate mutations primarily localized in the exopolysaccharide operon yjbEFGH. Collectively, our results show that selection from predatory bacteria can generate apparently stable sympatric phenotypic polymorphisms within coevolving prey populations and also allopatric diversity across populations by selecting for diverse mutations and colony phenotypes associated with mucoidy. More broadly, our results suggest that myxobacterial predation increases long-term diversity within natural microbial communities.

Bdellovibrio and like organisms: current understanding and knowledge gaps of the smallest cellular hunters of the microbial world

Almost sixty years ago, Bdellovibrio and like organisms (BALOs) were discovered as the first obligate bacterial predators of other bacteria known to science. Since then, they were shown to be diverse and ubiquitous in the environment, and to bear astonishing ecological, physiological, and metabolic capabilities. The last decade has seen important strides made in understanding the mechanistic basis of their life cycle, the dynamics of their interactions with prey, along with significant developments towards their use in medicine, agriculture, and industry. This review details these achievements, identify current understanding and knowledge gaps to encourage and guide future BALO research.

Taxonomic Compositions and Co-occurrence Relationships of Protists in Bulk Soil and Rhizosphere of Soybean Fields in Different Regions of China

As the main consumers of bacteria and fungi in farmed soils, protists remain poorly understood. The aim of this study was to explore protist community assembly and ecological roles in soybean fields. Here, we investigated differences in protist communities using high-throughput sequencing and their inferred potential interactions with bacteria and fungi between the bulk soil and rhizosphere compartments of three soybean cultivars collected from six ecological regions in China. Distinct protist community structures characterized the bulk soil and rhizosphere of soybean plants. A significantly higher relative abundance of phagotrophs was observed in the rhizosphere (25.1%) than in the bulk soil (11.3%). Spatial location (R 2 = 0.37-0.51) explained more of the variation in protist community structures of soybean fields than either the compartment (R 2 = 0.08-0.09) or cultivar type (R 2 = 0.02-0.03). The rhizosphere protist network (76 nodes and 414 edges) was smaller and less complex than the bulk soil network (147 nodes and 880 edges), indicating a smaller potential of niche overlap and interactions in the rhizosphere due to the increased resources in the rhizosphere. Furthermore, more inferred potential predator-prey interactions occur in the rhizosphere. We conclude that protists have a crucial ecological role to play as an integral part of microbial co-occurrence networks in soybean fields.

Microbial warfare in the wild-the impact of protists on the evolution and virulence of bacterial pathogens

During the long history of co-evolution with protists, bacteria have evolved defense strategies to avoid grazing and survive phagocytosis. These mechanisms allow bacteria to exploit phagocytic cells as a protective niche in which to escape from environmental stress and even replicate. Importantly, these anti-grazing mechanisms can function as virulence factors when bacteria infect humans. Here, we discuss how protozoan predation exerts a selective pressure driving bacterial virulence and shaping their genomes, and how bacteria-protist interactions might contribute to the spread of antibiotic resistance as well. We provide examples to demonstrate that besides being voracious bacterial predators, protozoa can serve as melting pots where intracellular organisms exchange genetic information, or even "training grounds" where some pathogens become hypervirulent after passing through. In this special issue, we would like to emphasize the tremendous impact of bacteria-protist interactions on human health and the potential of amoebae as model systems to study biology and evolution of a variety of pathogens. Besides, a better understanding of bacteria-protist relationships will help us expand our current understanding of bacterial virulence and, likely, how pathogens emerge.

Pseudomonas aeruginosa PA14 produces R-bodies, extendable protein polymers with roles in host colonization and virulence

R-bodies are long, extendable protein polymers formed in the cytoplasm of some bacteria; they are best known for their role in killing of paramecia by bacterial endosymbionts. Pseudomonas aeruginosa PA14, an opportunistic pathogen of diverse hosts, contains genes (referred to as the reb cluster) with potential to confer production of R-bodies and that have been implicated in virulence. Here, we show that products of the PA14 reb cluster associate with R-bodies and control stochastic expression of R-body structural genes. PA14 expresses reb genes during colonization of plant and nematode hosts, and R-body production is required for full virulence in nematodes. Analyses of nematode ribosome content and immune response indicate that P. aeruginosa R-bodies act via a mechanism involving ribosome cleavage and translational inhibition. Our observations provide insight into the biology of R-body production and its consequences during P. aeruginosa infection.

R-bodies are long, extendable protein polymers formed in the cytoplasm of some bacteria. Here, Wang et al. show that Pseudomonas aeruginosa produces R-bodies during colonization of plant and nematode hosts, and R-bodies induce ribosome cleavage and translational inhibition in nematodes.

Amoebae as Targets for Toxins or Effectors Secreted by Mammalian Pathogens

Numerous microorganisms, pathogenic for mammals, come from the environment where they encounter predators such as free-living amoebae (FLA). The selective pressure due to this interaction could have generated virulence traits that are deleterious for amoebae and represents a weapon against mammals. Toxins are one of these powerful tools that are essential for bacteria or fungi to survive. Which amoebae are used as a model to study the effects of toxins? What amoeba functions have been reported to be disrupted by toxins and bacterial secreted factors? Do bacteria and fungi effectors affect eukaryotic cells similarly? Here, we review some studies allowing to answer these questions, highlighting the necessity to extend investigations of microbial pathogenicity, from mammals to the environmental reservoir that are amoebae.

Phenanthrene degradation in soil using biochar hybrid modified bio-microcapsules: Determining the mechanism of action via comparative metagenomic analysis

A strategy involving biochar (BC) hybrid modification was developed to promote the bioremediation effect of degrading bacteria immobilized in layer-by-layer assembly (LBL) microcapsules for the treatment of phenanthrene (PHE) polluted soil. A taxonomic and functional metagenomic approach was used to investigate changes in the microbial community structures and functional gene compositions in the PHE-polluted soil during the bioremediation process. Biofortification with an initial PHE concentration of 100 mg kg^-1 dry soil in soils using the BC (3%) hybrid LBL bio-microcapsule (BC-LBL, 2.0 g kg^-1 dry soil, 10⁷ colony forming unite cell g^-1 dry soil) was faster; further, a higher PHE degradation efficiency (80.5% after 25 d) was achieved when compared with that by the LBL agent (66.2% after 25 d) used. Sphingomonas, Streptomyces, Gemmatirosa, Ramlibacter, Flavisolibacter, Phycicoccus, Micromonospora, Acidobacter, Mycobacterium and Gemmatimonas were more abundant in BC-LBL treatment than those in LBL one. Functional gene annotation results showed that more gene number with BC-LBL treatment than those with LBL one. More abundant functions in the former were primarily related to the growth, reproduction, metabolism, and transportation of bacteria. BC hybridization promoting PHE degradation by microencapsulated bacteria may be due to the strong adsorption property of BC, which results in the enrichment of the nutrients that needed for bacterial growth and reproduction, as well as enhancing the mass transfer performance of PHE to BC-LBL; Meanwhile, BC could also stimulate and improve the metabolism and membrane transportation of the degrading bacteria, and finally improving the degradation function.

On the phenology of protists: recurrent patterns reveal seasonal variation of protistan (Rhizaria: Cercozoa and Endomyxa) communities in tree canopies

Tree canopies are colonized by billions of highly specialized microorganisms that are well adapted to the highly variable microclimatic conditions, caused by diurnal fluctuations and seasonal changes. In this study, we investigated seasonality patterns of protists in the tree canopies of a temperate floodplain forest via high-throughput sequencing with group-specific primers for the phyla Cercozoa and Endomyxa. We observed consistent seasonality, and identified divergent spring and autumn taxa. Tree crowns were characterized by a dominance of bacterivores and omnivores, while eukaryvores gained a distinctly larger share in litter and soil communities on the ground. In the canopy seasonality was largest among communities detected on the foliar surface: In spring, higher variance within alpha diversity of foliar samples indicated greater heterogeneity during initial colonization. However, communities underwent compositional changes during the aging of leaves in autumn, highly reflecting recurring phenological changes during protistan colonization. Surprisingly, endomyxan root pathogens appeared to be exceptionally abundant across tree canopies during autumn, demonstrating a potential role of the canopy surface as a physical filter for air-dispersed propagules. Overall, about 80% of detected OTUs could not be assigned to known species-representing dozens of microeukaryotic taxa whose canopy inhabitants are waiting to be discovered.

The effect of polyhydroxyalkanoates in Pseudomonas chlororaphis PA23 biofilm formation, stress endurance, and interaction with the protozoan predator Acanthamoeba castellanii

Pseudomonas chlororaphis PA23 is a biocontrol agent capable of protecting canola against the fungal pathogen Sclerotinia sclerotiorum. In addition to producing antifungal compounds, this bacterium synthesizes and accumulates polyhydroxyalkanoate (PHA) polymers as carbon and energy storage compounds. Because the role of PHA in PA23 physiology is currently unknown, we investigated the impact of this polymer on stress resistance, adherence to surfaces, and interaction with the protozoan predator Acanthamoeba castellanii. Three PHA biosynthesis mutants were created, PA23phaC1, PA23phaC1ZC2, and PA23phaC1ZC2D, which accumulated reduced PHA. Our phenotypic assays revealed that PA23phaC1ZC2D produced less phenazine (PHZ) compared with the wild type (WT) and the phaC1 and phaC1ZC2 mutants. All three mutants exhibited enhanced sensitivity to UV irradiation, starvation, heat stress, cold stress, and hydrogen peroxide. Moreover, motility, exopolysaccharide production, biofilm formation, and root attachment were increased in strains with reduced PHA levels. Interaction studies with the amoeba A. castellanii revealed that the WT and the phaC1 and phaC1ZC2 mutants were consumed less than the phaC1ZC2D mutant, likely due to decreased PHZ production by the latter. Collectively these findings indicate that PHA accumulation enhances PA23 resistance to a number of stresses in vitro, which could improve the environmental fitness of this bacterium in hostile environments.